Hello bioconductor group, I have a FASTA sequences (without ID) and would like to find the homolge sequneces with BLAST. How can I do this in R explain me haw to do multiple sequence alignment with them. Thanks in advance, Zoha [[alternative HTML version deleted]]

Hi Zoha, On 11-06-06 07:49 AM, Zoha Moztarzadeh wrote: > Hello bioconductor group, > > I have a FASTA sequences (without ID) and would like to find the homolge sequneces with BLAST. > How can I do this in R explain me haw to do multiple sequence alignment with them. The only thing I'm aware of is the blastSequences() function in the annotate package. I've never used this function. Cheers, H. > > Thanks in advance, > > Zoha > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319

Dear Zoha, I think the simplest thing to do is to invoke the command line blast from R, using the option -m 8 to get tabular output that can be automatically parsed by read.table. Example: myPipe <- pipe( "blastall -p blastp -i text.fasta -d data.fasta" ) results <- read.table( myPipe ) colnames( blastResults ) <- c( "QueryID", "SubjectID", "Perc.Ident", "Alignment.Length", "Mismatches", "Gap.Openings", "Q.start", "Q.end", "S.start", "S.end", "E", "Bits" ) However, that way you will not get the actual alignments. Cheers, j. On Mon, Jun 6, 2011 at 4:49 PM, Zoha Moztarzadeh <zoha_mozt at="" yahoo.com=""> wrote: > Hello bioconductor group, > > I have a FASTA sequences (without ID) and would like to find the homolge sequneces with BLAST. > How can I do this in R explain me haw to do multiple sequence alignment with them. > > Thanks in advance, > > Zoha > ? ? ? ?[[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- -------- Dr. January Weiner 3 -------------------------------------- Max Planck Institute for Infection Biology Charit?platz 1 D-10117 Berlin, Germany Web?? : www.mpiib-berlin.mpg.de Tel? ?? : +49-30-28460514